As a player, you don't purchase items from the C-Store, you purchase C-Points (or rather, Zen, which is then converted into C-Points). Whatever you choose to buy with your C-Points then has nothing to do with your actual money. That purchase was fulfilled the second you converted your Zen to C-Points.

There is still a chance that you'll be able to swap ships; if you make a request to Cryptic. It's not like they'd lose out on anything. They still get their 2000 points worth of credit.